This is a list of references for software and instruments available to the MX users at MAX IV for data collection and processing. Please make sure that you include the appropriate references in your publications.

Beamline software and instrumentation

  • MXCuBE3: U. Mueller, M. Thunnissen, J. Nan, M. Eguiraun, F. Bolmsten, A. Milàn-Otero, M. Guijarro, M. Oscarsson, D. de Sanctis & G. Leonard (2017) MXCuBE3: A New Era of MX-Beamline Control Begins, Synchrotron Radiation News, 30, 22-27, DOI: 10.1080/08940886.2017.1267564
  • ISPyB: Delagenière S., Brenchereau P., Launer L., Ashton A.W., Leal R., Veyrier S., Gabadinho J., Gordon E.J., Jones S.D., Levik K.E., McSweeney S.M., Monaco S., Nanao M., Spruce D., Svensson O., Walsh M.A. and Leonard G.A. ISPyB: an information management system for synchrotron macromolecular crystallography. (2011) Bioinformatics. 27, 3186-3192.

Automated pipelines for data processing

  • EDNA: Incardona M.F., Bourenkov G.P., Levik K., Pieritz R.A., Popov A.N., Svensson O. EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis. (2009) J Synchrotron Radiat. 16, 872-879.
  • autoPROC: Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O., Paciorek, W., Womack, T. & Bricogne, G. Data processing and analysis with the autoPROC toolbox.(2011). Acta Cryst. D67, 293-302.
  • Fast DP/Fast EP: Winter G. and McAuley K.E. Automated data collection for macromolecular crystallography (2011) Methods 55, 81-93. doi: 10.1016/j.ymeth.2011.06.010.

Software included in PReSTO

You can find the list of software packages and programs included in PReSTO in the NSC site. Please acknowledge the individual packges that you use.

Other MX software installed at MAX IV

  • CCP4 package: Winn, M. D. et al. Overview of the CCP4 suite and current developments. (2011) Acta Cryst. D67, 235-242.
  • Coot: P. Emsley, B. Lohkamp, W.G. Scott and K. Cowtan. Features and Development of Coot (2010). Acta Cryst. D66 486-501.
  • DIALS: Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G. DIALS: implementation and evaluation of a new integration package (2018). Acta Cryst. D74, 85-97.
  • imosflm: Battye, T.G.G., Kontogiannis, L., Johnson, O., Powell, H.R. and Leslie A. G. W. IMosflm: a new graphical interface for diffraction-image processing with MOSFLM (2011). Acta Cryst. D67, 271-281.
  • Phenix: P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, R.W. Grosse-Kunstleve, A.J. McCoy, N.W. Moriarty, R. Oeffner, R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger, and P.H. Zwart. PHENIX: a comprehensive Python-based system for macromolecular structure solution (2010). Acta Cryst. D66, 213-221.
  • Shelxc/d/e/l: Sheldrick, G. M. A short history of SHELX (2008). Acta Cryst. A64, 112-122.
  • XDS and XSCALE: Kabsch, W. XDS. (2010) Acta Cryst. D66, 125-132; Kabsch, W. Integration, scaling, space-group assignment and post refinement (2010). Acta Cryst. D66, 133-144.